From chemistry-request@server.ccl.net Sun Dec 17 04:37:24 2000 Received: from fjohn.Stanford.EDU (fjohn.Stanford.EDU [171.64.38.72]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA09986 for ; Sun, 17 Dec 2000 04:37:24 -0500 Received: from localhost (greg@localhost) by fjohn.Stanford.EDU (8.9.3/8.9.3) with ESMTP id BAA11973 for ; Sun, 17 Dec 2000 01:37:15 -0800 Date: Sun, 17 Dec 2000 01:37:14 -0800 (PST) From: Greg Lakatos To: chemistry@ccl.net Subject: CHARMm and MPICH Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Everyone. Recently I've been trying to compile a parallelized CHARMm c27b2 executable with MPICH 1.2.0 on a two-machine RedHat 7 cluster and have run into some difficulty. In particular when compiling charmm the command: ./install.com gnu large mpich runs to completion, produces an executable, but never asks for the path to the mpich libraries. Moreover when charmm is run with the command: charmm -p4wd . -p4pg hosts < inputfile.inp > outfile.out where hosts contains: head 0 /ptemp/charmm head 1 /ptemp/charmm n01 1 /ptemp/charmm n01 1 /ptemp/charmm charmm issues an error over the p4wd and p4pg switches. When run without these switches, charmm runs but only uses a single CPU. Any help resolving these issues would be greatly appreciated. - Greg From chemistry-request@server.ccl.net Fri Dec 15 17:09:47 2000 Received: from jaguar.it.wsu.edu (root@jaguar.it.wsu.edu [134.121.0.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA01472 for ; Fri, 15 Dec 2000 17:09:47 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id OAA04170 for ; Fri, 15 Dec 2000 14:09:47 -0800 (PST) Message-ID: <004901c066e3$bbda0210$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: References: <001301c06607$51d10170$b4297986@chem.wsu.edu> Subject: Re: CCL:Linda on AMD & alternative Date: Fri, 15 Dec 2000 14:09:45 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hi fellow CCLers, sorry to waste bandwidth but I thought it prudent to correct and set the record straight regarding a previous post of mine. I erroneously attributed MPI + g98 to a group in Spain. The group is actually in Milan and it was MPI + g94. Here is the web-site of the original email posted to the Beowulf mailing list: http://www.beowulf.org/pipermail/beowulf/1999-May/004795.html The gentlemen's name is Scalmani Giovanni and his contact information is as follows: Scalmani Giovanni Giovanni@averell.umh.ac.be Service de Chimie des Materiaux Nouveaux Centre de Recherche en Electronique et Photonique Moleculaires Universite' de Mons-Hainaut Place du Parc, 20 Phone: ++32-(0)65-373361 B-7000 Mons (Belgium) Fax: ++32-(0)65-373366 Gain, sorry to waste the bandwidth with this correction... Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: "Phillip D. Matz" To: " FORLANI ROBERTO / CHIMICA (N. ORD.)" ; Sent: Thursday, December 14, 2000 11:51 AM Subject: CCL:Linda on AMD & alternative > Hi Roberto! > > Here in the Chemistry Dept. at Washington State University we have two > Athlon beowulfs running G98 and Linda on RH6.2. I'd be more than happy to > help you get your system up and running. To my knowledge Gaussian, Inc. > does not support any other internode communication protocols for Linux, > although I have heard that a research group in Spain has g98 running on MPI. > Drop me a line and we'll talk about this more. > > Respectfully, > Phillip Matz > > matz@wsunix.wsu.edu > > ----- Original Message ----- > From: " FORLANI ROBERTO / CHIMICA (N. ORD.)" > To: > Sent: Thursday, December 14, 2000 10:26 AM > Subject: CCL:Linda on AMD & alternative > > > > Hi all, > > I'm a chemistry student interested in running G98 on a beowulf > > cluster (AMD K7, redhat 6.2). Before buying a G98 license we'd > > like to run successfully Linda on this CPU. > > Is there someone who has experience on this kind of platform? > > To your knowledge does it exist any alternative to Linda? > > I've read something about the possibility to use MPI, in > > particular over dual processors motherboards (it was a commercial site but > > I missed the address), any help will be appreciate. > > > > Best regards, > > > > Roberto Forlani > > > > -- > > Department of Chemistry > > University of Ferrara > > > > > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Dec 15 18:34:09 2000 Received: from mail.lsd.ornl.gov (mail.lsd.ornl.gov [160.91.102.38]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA01794 for ; Fri, 15 Dec 2000 18:34:08 -0500 Received: from ornl.gov (mailbkup.lsd.ornl.gov [160.91.102.69]) by mail.lsd.ornl.gov (Postfix) with ESMTP id 30A8F14E90 for ; Fri, 15 Dec 2000 18:34:07 -0500 (EST) Sender: nxy@ornl.gov Message-ID: <3A3AAA6E.49668C0F@ornl.gov> Date: Fri, 15 Dec 2000 18:34:07 -0500 From: Dong Xu X-Mailer: Mozilla 4.72 [en] (X11; U; SunOS 5.6 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: PROSPECT 1.0 is available Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Announcement: Version 1.0 of PROSPECT ===================================== The Computational Protein Structure Group of Oak Ridge National Laboratory would like to announce the release of PROSPECT Version 1.0. PROSPECT (PROtein Structure Prediction and Evaluation Computer Toolkit) is a threading-based protein structure prediction system. PROSPECT is particularly designed to recognize structural folds whose sequence have no significant homology to the target sequence. For detailed information about PROSPECT, please check http://compbio.ornl.gov/structure/prospect/ PROSPECT has a number of unique features -- * The system guarantees to find the globally optimal alignments for a given energy function with any combination of the following terms: (1) mutation energy (including position-specific score matrix derived from multiple-sequence alignments), (2) singleton energy (including matching scores to the predicted secondary structures), (3) pairwise contact potential (distance dependent or independent), and (4) alignment gap penalties. * The system allows users to easily incorporate biological knowledge and constraints into the threading process to find optimal alignments under the specified constraints, which may include: - specified disulfide bonds - specified active sites - specified secondary structures - specified NOE restraints in NMR - specified gaps with no gap penalties * The system provides a prediction confidence assessment for each prediction based on a neural-net method and an evaluation of compactness of the predicted structure. * A Web-based interface is available to browse the threading alignments and 3D structures. PROSPECT is free of charge to academic users. Please contact the authors (Ying Xu at xyn@ornl.gov or Dong Xu at xud@ornl.gov) about the download information. For commercial users, please contact the authors for licensing information. Reference: Ying Xu and Dong Xu. Protein threading using PROSPECT: Design and evaluation. Proteins: Structure, Function, and Genetics. 40:343-354. 2000. From chemistry-request@server.ccl.net Sat Dec 16 13:45:29 2000 Received: from hotmail.com (f224.law7.hotmail.com [216.33.237.224]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06635 for ; Sat, 16 Dec 2000 13:45:29 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sat, 16 Dec 2000 10:43:15 -0800 Received: from 195.146.52.160 by lw7fd.law7.hotmail.msn.com with HTTP; Sat, 16 Dec 2000 18:43:15 GMT X-Originating-IP: [195.146.52.160] From: "Mansoor Namazian" To: chemistry@ccl.net Subject: Final structure in terms of initial Z-matrix Date: Sat, 16 Dec 2000 18:43:15 -0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 16 Dec 2000 18:43:15.0364 (UTC) FILETIME=[0CC62E40:01C06790] Dear Sir, When I optimize a molecule using Gaussian, sometimes I get the "Final structure in terms of initial Z-matrix:" at the end of output file and sometimes I don't, no matter what I specify in the route section. I'd like to get always "Final structure in terms of initial Z-matrix" at the end of output file. Can anyone help please? Many thanks in advance. Namazian _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Sat Dec 16 14:59:37 2000 Received: from avfw98.lundbeck.com (firewall.lundbeck.com [130.227.160.11]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA06895 for ; Sat, 16 Dec 2000 14:59:36 -0500 Received: from firewall.lundbeck.com [130.227.160.11] (HELO localhost) by avfw98.lundbeck.com (AltaVista Mail V2.0J/2.0J BL25J listener) id 0000_0246_3a3b_d73a_a50f; Sat, 16 Dec 2000 20:57:30 +0000 Received: from somewhere by smtpxd Sender: torleif@ccl.net Message-ID: <3A3BD429.ED8F67F8@lundbeck.com> Date: Sat, 16 Dec 2000 21:44:25 +0100 From: Torleif alternative account X-Mailer: Mozilla 4.75 [en] (X11; U; Linux 2.2.16-22 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Java chemistry and modelling tools - update Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Greetings, I have updated my overview of available java cmeistry tools. I apologize for the missing acknowledgements to all of the people who have sent me pointers, I will include a list at the next update. http://www.torleif.org/computing/index.html#JavaTools Have fun ! --- Jan -- Dr. Jan T. Pedersen H. Lundbeck A/S Ottiliavej 9 2500 Valby Copenhagen, Denmark phone : +45 36 44 24 25 ext 2887 email: jatp@lundbeck.com W^3: http://www.torleif.org From chemistry-request@server.ccl.net Sun Dec 17 06:51:58 2000 Received: from ibms.sinica.edu.tw (ibms.ibms.sinica.edu.tw [140.109.40.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA11296 for ; Sun, 17 Dec 2000 06:51:57 -0500 Received: from ibms (ibms [140.109.40.101]) by ibms.sinica.edu.tw (8.11.1/8.11.1) with ESMTP id eBHBjn905572 for ; Sun, 17 Dec 2000 19:45:49 +0800 (CST) Date: Sun, 17 Dec 2000 19:45:49 +0800 (CST) From: Sergey Noskov To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I have a big problems with memory allocation in CHARMM27b1 bothly on SGI and GNU platfoorms. Unfortunately, I need to make an aproximate normal mode analysis for medium sized protein ( 5362 atom in all hydrogen force field). Options like REDU CMP or DIMB diagonalization does not help in this program. CHARMM error output include a message like : expanded heap on ***** words problem with storage MALLOC set to 0.0 Program can create a reduced basis for normal mode analysis for example IC FIRST BOND SECOND BOND in order to leave out mode larger than 1000 cm-1 but crushed during the calculation on diagonalization matrix. Did anybody have the same problem and is it possible to fixed it without recompilation of CHARMM? With best regards, Sergey Sergey Noskov Institute of BioMedical Sciences Academia Sinica Taipei 11529,Taiwan R.O.C. tel:886-2-27899043 (work) 886-2-26510783 (home) fax:886-2-27887641 e-mail:syn@ibms.sinica.edu.tw From chemistry-request@server.ccl.net Sun Dec 17 09:15:34 2000 Received: from bellatrix.pcl.ox.ac.uk (root@bellatrix.pcl.ox.ac.uk [163.1.35.134]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA11791 for ; Sun, 17 Dec 2000 09:15:33 -0500 Received: from localhost (ben@localhost) by bellatrix.pcl.ox.ac.uk (8.9.3/8.8.7) with ESMTP id OAA08765; Sun, 17 Dec 2000 14:15:19 GMT Date: Sun, 17 Dec 2000 14:15:19 +0000 (GMT) From: Ben Webb To: Greg Lakatos cc: chemistry@ccl.net Subject: Re: CCL:CHARMm and MPICH In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 17 Dec 2000, Greg Lakatos wrote: > Recently I've been trying to compile a parallelized CHARMm c27b2 > executable with MPICH 1.2.0 on a two-machine RedHat 7 cluster and have > run into some difficulty. In particular when compiling charmm the > command: > > ./install.com gnu large mpich > > runs to completion, produces an executable, but never asks for the path > to the mpich libraries. This is because you need to tell install.com to compile an MPI binary with the "M" switch. The MPICH switch simply tells install.com which variety of MPI you're using. ./install.com gnu large m mpich should do the trick. (BTW, if you want to use QUANTUM, you'll need c27b3, as there are some bugs in the c27b2 implementation on GNU platforms.) > Moreover when charmm is run with the command: > > charmm -p4wd . -p4pg hosts < inputfile.inp > outfile.out > > charmm issues an error over the p4wd and p4pg switches. CHARMM's command line argument handling is a bit suspect, so even a binary linked properly to the MPICH libraries will give warnings for some MPICH options (see source/machdep/startup.src for details) but these can be safely ignored. CHARMM compiled _with_ the M switch should at least only treat them as warnings, not errors, though! (Oh, and another thing about using MPICH - I would recommend explicitly specifying the number of processors with -np, or, better still, running your binary via. mpirun.) Ben -- ben@bellatrix.pcl.ox.ac.uk http://bellatrix.pcl.ox.ac.uk/~ben/ "Public speaking is very easy." - Vice President Dan Quayle From chemistry-request@server.ccl.net Sun Dec 17 17:36:15 2000 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA14111 for ; Sun, 17 Dec 2000 17:36:14 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA05410; Sun, 17 Dec 2000 17:23:53 -0500 (EST) Date: Sun, 17 Dec 2000 17:23:53 -0500 From: Rick Venable To: Sergey Noskov cc: chemistry@ccl.net Subject: Re: No Subject Given By The Author In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 17 Dec 2000, Sergey Noskov wrote: > I have a big problems with memory allocation in CHARMM27b1 bothly on SGI > and GNU platfoorms. Unfortunately, I need to make an aproximate normal > mode analysis for medium sized protein ( 5362 atom in all hydrogen force > field). Options like REDU CMP or DIMB diagonalization does not help in > this program. CHARMM error output include a message like : > > expanded heap on ***** words > problem with storage > MALLOC set to 0.0 This indicates that CHARMM asked for some extra memory, which the OS could not provide. Since normal modes require a 3N*3N matrix, the memory needed in Mbytes is (8*(3*N)**2)/(1024*1024) for N=5362 = 1974 or almost 2 Gbytes of memory. Your system (IRIX or Linux) needs to have a fairly large amount of physical RAM and more that 2 Gbyte of swap space configured in order to do this calculation. -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or Rick_Venable@nih.gov | \ / |=| position of the FDA; for that, rvenable@speakeasy.org \/ |=| see http://www.fda.gov ) From chemistry-request@server.ccl.net Sun Dec 17 14:42:35 2000 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA13513 for ; Sun, 17 Dec 2000 14:42:34 -0500 Received: from jove.acs.unt.edu (10759@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id NAA13923 for ; Sun, 17 Dec 2000 13:42:31 -0600 (CST) Received: from localhost (tdp0006@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id NAA01265 for ; Sun, 17 Dec 2000 13:42:27 -0600 (CST) Date: Sun, 17 Dec 2000 13:42:26 -0600 (CST) From: TREVOR D POWER To: chemistry@ccl.net Subject: Re: CCL:Final structure in terms of initial Z-matrix Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Namazian, What version of Gaussian are you using? 94? Are you employing dummy atoms in the construction of you input file? I am not really sure what "Final structure in terms of initial Z-matrix" implies. If you specify a geometry in the input.file as a Z-matrix in either Gaussian 94 or Gaussian 98 without using opt=z-matrix the input geometry with be converted to redundant internal coordinates and the output parameters of the optimized geometry will not necessarily correspond to those in the input z-matrix. By default, Gaussian 92 interpreted opt (in the route card) as opt=z-matrix. You should note that opt=z-matrix is a very poor manner in which to obtain an optimized geometry because 1) the program will take forever to optimize the geometry based on just those parameters you specify in the input.file and 2) you have a very good chance of obtaining a local minumum as a result of inherent constrainst this technique employs. What I would do is specify opt=addredun (Gaussian 94) or opt=modredun (Gaussian 98) and at the end of the geometry input section of the input file explicity list those redundant coordinates you wish to see (in addition to those the program selects) in the output file. You will, of course, need to know what the approximate values are for these parameters so as to not perturb your initial geometry too much: 1 2 1.43 (for bond length) 1 2 3 120.0 (for angle) 1 2 3 4 34.0 (for dihedral angle) where 1, 2, 3 and 4 are atoms specified. If you use dummy atoms in the input, you cannot use these to construct these coordinates as dummy atoms are deleted once the geometry is read into the program and the molecule is transulated into redundant internal coordinates. You can get additional bond lengths from the distance matrix in the output.file. Also there is a way to print all angles and all dihedrals. If you are interested in that I can dig this up later. Hope this helped, David Power Department of Chemistry Univerity of North Texas NT Staion, Box 305070 Denton, Texas 76203-5070 tdp0006@unt.edu On Sat, 16 Dec 2000, Mansoor Namazian wrote: > Dear Sir, > > When I optimize a molecule using Gaussian, sometimes I get > the "Final structure in terms of initial Z-matrix:" at the > end of output file and sometimes I don't, no matter what > I specify in the route section. > I'd like to get always "Final structure in terms of initial > Z-matrix" at the end of output file. Can anyone help please? > > Many thanks in advance. > Namazian > > _________________________________________________________________________ > Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Sun Dec 17 22:06:55 2000 Received: from linux2.ipc.pku.edu.cn (mao@linux2.ipc.pku.edu.cn [162.105.177.40]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA15072 for ; Sun, 17 Dec 2000 22:06:52 -0500 Received: from localhost (mao@localhost) by linux2.ipc.pku.edu.cn (8.9.3/8.9.3) with ESMTP id LAA02538 for ; Mon, 18 Dec 2000 11:14:55 +0800 Date: Mon, 18 Dec 2000 11:14:55 +0800 (CST) From: Fenglou Mao To: "CHEMISTRY@www.ccl.net" Subject: best secondary structure prediction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, all, Can anyone tell me what is the best secondary structure prediction method include the method name and the correct ratio? Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Institute of Physical Chemistry Peking University BeiJing P.R.China Tel:86-10-62756833 Fax:86-10-62751725 E-mail:mao@mdl.ipc.pku.edu.cn Homepage:http://mdl.ipc.pku.edu.cn/~mao From chemistry-request@server.ccl.net Sun Dec 17 22:53:25 2000 Received: from wilson.acpub.duke.edu (wilson.acpub.duke.edu [152.3.233.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA15234 for ; Sun, 17 Dec 2000 22:53:25 -0500 Received: from ZhenyuLu (dhcp9141.chem.duke.edu [152.3.169.141]) by wilson.acpub.duke.edu (8.9.3/8.9.3/Duke-5.0.0) with SMTP id WAA11543; Sun, 17 Dec 2000 22:53:19 -0500 (EST) Message-ID: <002601c068a5$e87be4a0$8da90398@chem.duke.edu> From: "Zhenyu Lu" To: Subject: IRC reaction path geometres Date: Sun, 17 Dec 2000 22:52:13 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0023_01C0687B.FF398640" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0023_01C0687B.FF398640 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I was using Gaussian 98, ran reaction path calculations. I used keyword IRC, doing forward and backword reactons.=20 In the gaussian output file, you will see geometres and energes of each point are listed as a table.=20 My question is: How can I convert one Gaussian output file to PDB files or XYZ files, each PDB/XYZ file for just one point along the reaction path? I know Gaussian provides some unitily, like newzmat, which can =20 make a convertion between different file types, but I don't know how to = use it to solve my question above. Thanks in advance. Zhenyu Lu Dept of Chem, Duke Univ. =20 ------=_NextPart_000_0023_01C0687B.FF398640 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi, I was using Gaussian 98, ran reaction path=20 calculations.
I used keyword IRC, doing forward and backword = reactons.=20
In the gaussian output file, you will=20  see geometres and energes
of each point are listed as a table.
My question is:
How can I convert one Gaussian output=20 file  to PDB files or XYZ
files,  each PDB/XYZ =  file=20 for just one point along the reaction path?
 
I know Gaussian provides some unitily, like=20 newzmat, which can  
make a convertion between different file  = types, but I=20 don't know how to use it
to solve my question above.
 
Thanks in advance.
Zhenyu Lu
Dept of Chem, Duke Univ.
 
 
 
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